By combining the clinically proven and well-established associations between the two genes, i.e., NUDT15 and TPMT, and 6-MP dose intensity percent (DIP, actual/planned dose) as a clinical endpoint, we performed a comparison study of the conventional star allele-based haplotyping and GVB scoring methods for predicting the last-cycle 6-MP DIP as an indicator for 6-MP intolerance of ALL patients with NUDT15 and/or TPMT deficiency. The gene discussed is TPMT; the disease is acute lymphoblastic leukemia.